Disease model systems, such as the zebrafish, play an important role in understanding the onset of diseases like cancer and monitor the efficacy of new drugs. In the past, non-invasive methods for screening, diagnostics and treatment monitoring were intrinsically from the outside. In the past decades, there has been a strong drive to look inside these model systems, which resulted in the development of many small animal tomographic imaging techniques. Due to the absence of ionizing radiation, high-resolution, and cost efficiency, optical tomography is a popular imaging technique to study disease model systems such as zebrafish. The main obstacles in obtaining high-resolution imaging suitable for tissue characterization are the scattering of light in tissue and diffraction of optical waves. Scattering of light in tissue degrades the resolution of optical tomography systems, especially for thick samples. In this thesis, transmission optical coherence tomography (OCT) is used to select ballistic, non-scattered, from non-ballistic, scattered, light. We demonstrate that transmission optical coherence tomography is a versatile tool to measure optical properties of liquids, solids, and particle suspensions. The developed technique is used to perform quantitative optical tomography of the refractive index and attenuation coefficient. A good agreement is observed between our measurements and literature values for group refractive index, group velocity dispersion, and attenuation coefficient. Based on the tomographic reconstruction of transmission OCT measurements, the median attenuation coefficient, group refractive index and volumes of various organs of an adult zebrafish are segmented and quantified in optical coherence projection tomography reconstructions. In optical tomography light is imaged by a lens onto the camera. Due to the focusing of light onto the camera, this light is collected non-uniformly along the propagation direction from the sample. Consequently, the straight-ray assumption as in standard (pre-) clinical X-ray CT reconstruction is violated. Reconstruction of optical tomography images with standard filtered back projection (FBP) causes radial blurring and tangential blurring that becomes stronger with increasing distance to the rotation axis. We present 2D and 3D tomographic reconstruction algorithms that include the point spread function (PSF) of the imaging system. For emission optical projection tomography, these methods show greatly reduced radial and tangential blurring over the entire field of view 113 114 Summary and a significantly improved signal-to-noise ratio compared to FBP. The 3D PSF-based algorithm is evaluated using different initializations. When initialized with the 2D PSF-based reconstruction result, the 3D PSF-based reconstruction gives an improved signal-to-background and image quality in a useful timeframes. Besides including the physical point spread function (PSF) in the 2D tomographic reconstruction, the effect of the PSF also can be reduced by deconvolution of the FBP reconstructed image or filtering the sinogram before FBP reconstruction. We compared the performance of these techniques with each other based on simulations and the signal-to-noise ratio and the sharpness in reconstructed fluorescent beads and zebrafish OPT images. We demonstrate that the sinogram filtering performs poorly on data acquired with high numerical aperture optical imaging systems. We show that the deconvolution technique performs best for highly sparse, low signal-to-noise ratio objects. The PSF-based reconstruction method is superior for non-sparse objects and data of high signal-to-noise ratio. In this thesis, we developed novel algorithms for transmission OCT signal processing and PSF-based tomographic reconstruction. Our algorithms allow for high-resolution quantitative imaging in turbid media. These techniques can be used for quantitative optical imaging of disease model systems. Potentially this may lead to more insight in tissue development and disease onset, progression, and treatment.